The entire point of the monorail was that it is the living embodiment of the legacy of Thomas Wayne. Public transportation is at heart the most egalitarian project a city can construct and represented Wayne's hope for the common people of Gotham city. It also symbolized his brand of activism in trying to "save" the city.

Seeing as how the point of the first movie was Bruce trying to make sense of that legacy and ultimately deciding to go a different, more disturbing (but perhaps more effective at the end) path... to the point of PHYSICALLY destroying the embodiment of his father's legacy... the monorail has jack to do with the 2nd movie so it isn't featured in TDK

Funilly enough the monorail does live on in SPIRIT in the 2nd movie. If it represents a clean, legitimate, through-the-laws HOPE for the people of Gotham, the "monorail" in the 2nd movie is Harvey Dent.